If you're referring to the Reconcile Now option, that's for BES. If you open an email on your mailbox it should show opened on your device, if it doesn't happen instantly, you can select that option and it will reconcile your device to mark the items read. That's just a brief example.

__________________The difference between stupidity and genius is that genius has its limits.When you take things for granted, the things you are granted, get taken. Even a mosquito doesn't get a pat on the back until it starts to work.Too many people miss the silver lining because they're expecting gold.[BES 5.0.3 / GroupWise 2012 HP2]

If you're referring to the Reconcile Now option, that's for BES. If you open an email on your mailbox it should show opened on your device, if it doesn't happen instantly, you can select that option and it will reconcile your device to mark the items read. That's just a brief example.

As I understand that function, using BIS, when you hit "Reconcile Now", email deleted on the BB will also be deleted on your email server. Generally this is done when RIM polls for email the next cycle after you hit that option.

It does nothing to mail already downloaded to your PC's email client however.